Only the 1/3 portion of the Coronavirus-Related Distribution (CRD) that is included on your 2020 tax return adds to your taxable income from which your 2020 tax liability is determined.
If you have the ability to repay some of the CRD before the due date of your 2020 tax return, including extensions, the amount repaid will directly reduce the amount of the CRD that is includible in income on your 2020 tax return, reducing underpayment penalties that otherwise might have already accrued.
It's too late to make an estimated tax payments for 2020 to reduce the amount of underpayment penalty that has already accrued to date, but the sooner you pay your balance due the less additional penalty you'll accrue. The only reason to make an estimated tax payment for 2020 now would be if you are still not ready to file your 2020 tax return and just pay the balance due.
